Related papers: On reversible and reversible-complementary DNA cod…
The coding problem considered in this work is to construct a linear code $\mathcal{C}$ of given length $n$ and dimension $k<n$ such that a given binary vector $\mathbf{r} \in \mathbb{F}^{n}$ is contained in the code. We study a recent…
We consider the problem of counting the copies of a length-$k$ pattern $\sigma$ in a sequence $f \colon [n] \to \mathbb{R}$, where a copy is a subset of indices $i_1 < \ldots < i_k \in [n]$ such that $f(i_j) < f(i_\ell)$ if and only if…
In this work, we define a modification of a bordered construction for self-dual codes which utilises $\lambda$-circulant matrices. We provide the necessary conditions for the construction to produce self-dual codes over finite commutative…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
A linear code of length $n$ over a finite chain ring $R$ with residue field $\F_q$ is a $R$-submodule of $R^n$. A $R$-linear code is a code over $\F_q$ (not necessarily linear) which is the generalized Gray map image of a linear code over…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
The notion of universally decodable matrices (UDMs) was recently introduced by Tavildar and Viswanath while studying slow fading channels. It turns out that the problem of constructing UDMs is tightly connected to the problem of…
We show that the sequence of dimensions of the linear spaces, generated by a given rank-metric code together with itself under several applications of a field automorphism, is an invariant for the whole equivalence class of the code. These…
DNA cloning methods are fundamental tools in molecular biology, synthetic biology, and genetic engineering that enable precise DNA manipulation for various scientific and biotechnological applications. This review systematically summarizes…
The problem of storing permutations in a distributed manner arises in several common scenarios, such as efficient updates of a large, encrypted, or compressed data set. This problem may be addressed in either a combinatorial or a coding…
In this work, we define composite matrices which are derived from group rings. We extend the idea of G-codes to composite G-codes. We show that these codes are ideals in a group ring, where the ring is a finite commutative Frobenius ring…
A hierarchical, reversible mapping between levels of tree structured computation, applicable for structuring the Quantum Computation algorithm for NP-complete problem is presented. It is proven that confining the state of a quantum computer…
Non-overlapping codes have been studied for almost 60 years. In such a code, no proper, non-empty prefix of any codeword is a suffix of any codeword. In this paper, we study codes in which overlaps of certain specified sizes are forbidden.…
For $(n,d)= (66,17),(78,19)$ and $(94,21)$, we construct quantum $[[n,0,d]]$ codes which improve the previously known lower bounds on the largest minimum weights among quantum codes with these parameters. These codes are constructed from…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
We define two extensions of the typed linear lambda-calculus that yield minimal Turing-complete systems. The extensions are based on unbounded recursion in one case, and bounded recursion with minimisation in the other. We show that both…